Pseudotime heatmaps of significant transcription factors
q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes: 1983
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 100
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)

plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf
## 2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
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gene
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1
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2
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3
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4
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5
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6
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7
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8
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9
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10
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11
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14
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25
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27
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28
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29
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30
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31
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32
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33
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34
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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58
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59
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60
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61
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62
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63
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64
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65
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66
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67
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68
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69
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70
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71
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72
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73
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74
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75
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76
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77
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78
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80
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81
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82
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84
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85
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86
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87
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88
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
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100
|
|
Smarcc1
|
1.9808307
|
1.8869484
|
1.7938039
|
1.7015379
|
1.6102875
|
1.5201861
|
1.4313635
|
1.3439458
|
1.2580556
|
1.1738123
|
1.0913316
|
1.0107264
|
0.9321062
|
0.8555779
|
0.7812455
|
0.7092104
|
0.6395719
|
0.5724270
|
0.5078707
|
0.4459967
|
0.3868969
|
0.3306623
|
0.2773830
|
0.2271487
|
0.1800486
|
0.1361722
|
0.0956094
|
0.0584508
|
0.0247883
|
-0.0052847
|
-0.0316731
|
-0.0542793
|
-0.0730029
|
-0.0877404
|
-0.0983847
|
-0.1048246
|
-0.1069443
|
-0.1046231
|
-0.0977396
|
-0.0863791
|
-0.0709098
|
-0.0517172
|
-0.0291857
|
-0.0036999
|
0.0243545
|
0.0545896
|
0.0866143
|
0.1200337
|
0.1544486
|
0.1894550
|
0.2246437
|
0.2596007
|
0.2939066
|
0.3271373
|
0.3588640
|
0.3886541
|
0.4160712
|
0.4406768
|
0.4620304
|
0.4796913
|
0.4932192
|
0.5021763
|
0.5061283
|
0.5046465
|
0.4973095
|
0.4837051
|
0.4634327
|
0.4361055
|
0.4013530
|
0.3589047
|
0.3089514
|
0.2518468
|
0.1879541
|
0.1176447
|
0.0412961
|
-0.0407097
|
-0.1279873
|
-0.2201496
|
-0.3168091
|
-0.4175796
|
-0.5220771
|
-0.6299211
|
-0.7407360
|
-0.8541523
|
-0.9698073
|
-1.0873463
|
-1.206424
|
-1.326704
|
-1.447861
|
-1.569581
|
-1.691563
|
-1.813517
|
-1.935167
|
-2.056248
|
-2.176512
|
-2.295724
|
-2.413660
|
-2.530114
|
-2.644891
|
-2.757812
|
|
Hmgb3
|
2.4847649
|
2.3612506
|
2.2387326
|
2.1174024
|
1.9974462
|
1.8790451
|
1.7623746
|
1.6476046
|
1.5348988
|
1.4244149
|
1.3163042
|
1.2107117
|
1.1077761
|
1.0076296
|
0.9103980
|
0.8162010
|
0.7251522
|
0.6373594
|
0.5529251
|
0.4719463
|
0.3945154
|
0.3207206
|
0.2506463
|
0.1843737
|
0.1219813
|
0.0635460
|
0.0091434
|
-0.0411514
|
-0.0872628
|
-0.1291139
|
-0.1666258
|
-0.1997166
|
-0.2283003
|
-0.2522862
|
-0.2715777
|
-0.2860713
|
-0.2956557
|
-0.3002109
|
-0.2996120
|
-0.2939440
|
-0.2835798
|
-0.2689060
|
-0.2503046
|
-0.2281552
|
-0.2028372
|
-0.1747311
|
-0.1442210
|
-0.1116951
|
-0.0775473
|
-0.0421779
|
-0.0059941
|
0.0305894
|
0.0671503
|
0.1032591
|
0.1384791
|
0.1723667
|
0.2044727
|
0.2343427
|
0.2615183
|
0.2855386
|
0.3059414
|
0.3222647
|
0.3340489
|
0.3408387
|
0.3421850
|
0.3376477
|
0.3267982
|
0.3092223
|
0.2845236
|
0.2524084
|
0.2130510
|
0.1667939
|
0.1139934
|
0.0550179
|
-0.0097534
|
-0.0799318
|
-0.1551210
|
-0.2349178
|
-0.3189145
|
-0.4066995
|
-0.4978594
|
-0.5919805
|
-0.6886505
|
-0.7874598
|
-0.8880040
|
-0.9898850
|
-1.092713
|
-1.196109
|
-1.299705
|
-1.403148
|
-1.506099
|
-1.608237
|
-1.709258
|
-1.808881
|
-1.906841
|
-2.002899
|
-2.096836
|
-2.188458
|
-2.277591
|
-2.364086
|
|
Ybx1
|
2.2362754
|
2.1428771
|
2.0496497
|
1.9567171
|
1.8642029
|
1.7722303
|
1.6809226
|
1.5904026
|
1.5007928
|
1.4122155
|
1.3247930
|
1.2386470
|
1.1538992
|
1.0706709
|
0.9890833
|
0.9092575
|
0.8313140
|
0.7553736
|
0.6815566
|
0.6099832
|
0.5407735
|
0.4740475
|
0.4099249
|
0.3485256
|
0.2899692
|
0.2343753
|
0.1818634
|
0.1325532
|
0.0865642
|
0.0440160
|
0.0050284
|
-0.0302788
|
-0.0617858
|
-0.0893724
|
-0.1129183
|
-0.1323032
|
-0.1474061
|
-0.1581061
|
-0.1642863
|
-0.1660197
|
-0.1636363
|
-0.1574839
|
-0.1479101
|
-0.1352624
|
-0.1198880
|
-0.1021344
|
-0.0823490
|
-0.0608791
|
-0.0380725
|
-0.0142768
|
0.0101600
|
0.0348897
|
0.0595640
|
0.0838343
|
0.1073519
|
0.1297677
|
0.1507326
|
0.1698974
|
0.1869126
|
0.2014287
|
0.2130963
|
0.2215659
|
0.2264881
|
0.2275139
|
0.2242942
|
0.2164805
|
0.2037247
|
0.1856792
|
0.1619970
|
0.1323972
|
0.0969565
|
0.0558735
|
0.0093473
|
-0.0424226
|
-0.0992364
|
-0.1608941
|
-0.2271955
|
-0.2979401
|
-0.3729276
|
-0.4519574
|
-0.5348290
|
-0.6213421
|
-0.7112963
|
-0.8044913
|
-0.9007274
|
-0.9998046
|
-1.101524
|
-1.205685
|
-1.312090
|
-1.420541
|
-1.530838
|
-1.642786
|
-1.756186
|
-1.870842
|
-1.986558
|
-2.103138
|
-2.220388
|
-2.338113
|
-2.456120
|
-2.574216
|
|
Nr2e1
|
1.8781158
|
1.7899168
|
1.7033417
|
1.6184981
|
1.5354848
|
1.4543924
|
1.3753031
|
1.2982918
|
1.2234262
|
1.1507672
|
1.0803696
|
1.0122825
|
0.9465500
|
0.8832112
|
0.8223012
|
0.7638516
|
0.7078905
|
0.6544438
|
0.6035351
|
0.5551864
|
0.5094188
|
0.4662529
|
0.4257092
|
0.3878087
|
0.3525736
|
0.3200277
|
0.2901968
|
0.2631096
|
0.2387979
|
0.2172976
|
0.1986487
|
0.1828967
|
0.1700925
|
0.1602936
|
0.1535648
|
0.1499786
|
0.1496163
|
0.1525691
|
0.1589338
|
0.1686224
|
0.1812888
|
0.1965715
|
0.2141081
|
0.2335330
|
0.2544747
|
0.2765539
|
0.2993818
|
0.3225591
|
0.3456752
|
0.3683083
|
0.3900256
|
0.4103843
|
0.4289329
|
0.4452134
|
0.4587638
|
0.4691213
|
0.4758262
|
0.4784258
|
0.4764798
|
0.4695650
|
0.4572814
|
0.4392584
|
0.4151611
|
0.3846964
|
0.3476205
|
0.3037447
|
0.2529421
|
0.1951534
|
0.1303920
|
0.0588267
|
-0.0188878
|
-0.1019332
|
-0.1894895
|
-0.2807456
|
-0.3749092
|
-0.4712148
|
-0.5689318
|
-0.6673707
|
-0.7658882
|
-0.8638915
|
-0.9608411
|
-1.0562527
|
-1.1496981
|
-1.2408052
|
-1.3292566
|
-1.4147884
|
-1.497187
|
-1.576289
|
-1.651972
|
-1.724159
|
-1.792806
|
-1.857907
|
-1.919482
|
-1.977580
|
-2.032268
|
-2.083636
|
-2.131786
|
-2.176833
|
-2.218902
|
-2.258125
|
|
Pax6
|
1.3558933
|
1.3044440
|
1.2536696
|
1.2036512
|
1.1544660
|
1.1061876
|
1.0588856
|
1.0126262
|
0.9674723
|
0.9234836
|
0.8807168
|
0.8392258
|
0.7990622
|
0.7602751
|
0.7229115
|
0.6870168
|
0.6526346
|
0.6198074
|
0.5885764
|
0.5589822
|
0.5310649
|
0.5048643
|
0.4804203
|
0.4577730
|
0.4369636
|
0.4180338
|
0.4010269
|
0.3859878
|
0.3729633
|
0.3620027
|
0.3531580
|
0.3464842
|
0.3420399
|
0.3398879
|
0.3400950
|
0.3427334
|
0.3478804
|
0.3556193
|
0.3660359
|
0.3790354
|
0.3942734
|
0.4113854
|
0.4300027
|
0.4497502
|
0.4702453
|
0.4910965
|
0.5119028
|
0.5322539
|
0.5517303
|
0.5699039
|
0.5863397
|
0.6005972
|
0.6122329
|
0.6208035
|
0.6258683
|
0.6269941
|
0.6237587
|
0.6157562
|
0.6026018
|
0.5839372
|
0.5594367
|
0.5288129
|
0.4918226
|
0.4482728
|
0.3980265
|
0.3410080
|
0.2772082
|
0.2066883
|
0.1295841
|
0.0461821
|
-0.0427670
|
-0.1363669
|
-0.2337320
|
-0.3339992
|
-0.4363369
|
-0.5399539
|
-0.6441061
|
-0.7481025
|
-0.8513095
|
-0.9531540
|
-1.0531251
|
-1.1507751
|
-1.2457187
|
-1.3376318
|
-1.4262491
|
-1.5113616
|
-1.592813
|
-1.670494
|
-1.744343
|
-1.814335
|
-1.880483
|
-1.942829
|
-2.001443
|
-2.056417
|
-2.107862
|
-2.155903
|
-2.200679
|
-2.242334
|
-2.281020
|
-2.316891
|
|
Nfia
|
1.2369566
|
1.2055009
|
1.1741786
|
1.1430303
|
1.1120963
|
1.0814162
|
1.0510293
|
1.0209742
|
0.9912893
|
0.9620122
|
0.9331802
|
0.9048301
|
0.8769983
|
0.8497208
|
0.8230330
|
0.7969700
|
0.7715665
|
0.7468569
|
0.7228752
|
0.6996551
|
0.6772301
|
0.6556332
|
0.6348976
|
0.6150558
|
0.5961407
|
0.5781846
|
0.5612201
|
0.5452795
|
0.5303955
|
0.5166005
|
0.5039271
|
0.4924083
|
0.4820771
|
0.4729669
|
0.4651114
|
0.4585447
|
0.4533014
|
0.4494166
|
0.4469235
|
0.4457509
|
0.4456862
|
0.4465074
|
0.4479925
|
0.4499198
|
0.4520674
|
0.4542132
|
0.4561348
|
0.4576098
|
0.4584154
|
0.4583291
|
0.4571286
|
0.4545920
|
0.4504984
|
0.4446282
|
0.4367634
|
0.4266883
|
0.4141900
|
0.3990592
|
0.3810907
|
0.3600843
|
0.3358459
|
0.3081878
|
0.2769307
|
0.2419039
|
0.2029470
|
0.1599112
|
0.1126607
|
0.0610739
|
0.0050453
|
-0.0554683
|
-0.1202524
|
-0.1890022
|
-0.2614083
|
-0.3371570
|
-0.4159322
|
-0.4974159
|
-0.5812897
|
-0.6672361
|
-0.7549396
|
-0.8440878
|
-0.9343730
|
-1.0254934
|
-1.1171542
|
-1.2090690
|
-1.3009610
|
-1.3925642
|
-1.483625
|
-1.573901
|
-1.663167
|
-1.751209
|
-1.837831
|
-1.922851
|
-2.006106
|
-2.087448
|
-2.166747
|
-2.243888
|
-2.318775
|
-2.391327
|
-2.461479
|
-2.529182
|
|
Zfp36l1
|
1.1006416
|
1.0749335
|
1.0493636
|
1.0239739
|
0.9988057
|
0.9738998
|
0.9492962
|
0.9250344
|
0.9011530
|
0.8776903
|
0.8546838
|
0.8321704
|
0.8101866
|
0.7887681
|
0.7679504
|
0.7477681
|
0.7282558
|
0.7094473
|
0.6913764
|
0.6740761
|
0.6575796
|
0.6419197
|
0.6271288
|
0.6132397
|
0.6002847
|
0.5882963
|
0.5773072
|
0.5673501
|
0.5584581
|
0.5506645
|
0.5440032
|
0.5385083
|
0.5342148
|
0.5311582
|
0.5293749
|
0.5289021
|
0.5297778
|
0.5320414
|
0.5357301
|
0.5407452
|
0.5468029
|
0.5536060
|
0.5608558
|
0.5682523
|
0.5754937
|
0.5822767
|
0.5882963
|
0.5932467
|
0.5968212
|
0.5987135
|
0.5986182
|
0.5962317
|
0.5912541
|
0.5833898
|
0.5723497
|
0.5578526
|
0.5396273
|
0.5174150
|
0.4909715
|
0.4600700
|
0.4245041
|
0.3840909
|
0.3386747
|
0.2881309
|
0.2323696
|
0.1713407
|
0.1050382
|
0.0335052
|
-0.0431615
|
-0.1247494
|
-0.2106877
|
-0.3002786
|
-0.3928125
|
-0.4875745
|
-0.5838515
|
-0.6809394
|
-0.7781515
|
-0.8748264
|
-0.9703362
|
-1.0640944
|
-1.1555635
|
-1.2442609
|
-1.3297646
|
-1.4117170
|
-1.4898275
|
-1.5638726
|
-1.633696
|
-1.699204
|
-1.760364
|
-1.817198
|
-1.869776
|
-1.918212
|
-1.962653
|
-2.003275
|
-2.040276
|
-2.073866
|
-2.104268
|
-2.131706
|
-2.156407
|
-2.178589
|
|
Gsx1
|
0.8215144
|
0.7712369
|
0.7218386
|
0.6734419
|
0.6261614
|
0.5801040
|
0.5353696
|
0.4920512
|
0.4502360
|
0.4100051
|
0.3714348
|
0.3345967
|
0.2995583
|
0.2663841
|
0.2351356
|
0.2058726
|
0.1786533
|
0.1535356
|
0.1305772
|
0.1098370
|
0.0913754
|
0.0752553
|
0.0615430
|
0.0503091
|
0.0416293
|
0.0355853
|
0.0322661
|
0.0317693
|
0.0342014
|
0.0396802
|
0.0483352
|
0.0603100
|
0.0757630
|
0.0948699
|
0.1178253
|
0.1448448
|
0.1761674
|
0.2120583
|
0.2528040
|
0.2984172
|
0.3485020
|
0.4026098
|
0.4602590
|
0.5209276
|
0.5840466
|
0.6489951
|
0.7150959
|
0.7816133
|
0.8477522
|
0.9126587
|
0.9754237
|
1.0350869
|
1.0906448
|
1.1410599
|
1.1852721
|
1.2222131
|
1.2508223
|
1.2700655
|
1.2789550
|
1.2765716
|
1.2620879
|
1.2347931
|
1.1941172
|
1.1396565
|
1.0711971
|
0.9887374
|
0.8925075
|
0.7829849
|
0.6609053
|
0.5274109
|
0.3846293
|
0.2349841
|
0.0808469
|
-0.0755136
|
-0.2319779
|
-0.3866141
|
-0.5377079
|
-0.6837840
|
-0.8236184
|
-0.9562409
|
-1.0809299
|
-1.1971996
|
-1.3047808
|
-1.4035979
|
-1.4937422
|
-1.5754444
|
-1.649046
|
-1.714975
|
-1.773716
|
-1.825795
|
-1.871755
|
-1.912142
|
-1.947493
|
-1.978322
|
-2.005121
|
-2.028345
|
-2.048415
|
-2.065719
|
-2.080605
|
-2.093385
|
|
Etv1
|
0.9260086
|
0.8835890
|
0.8416401
|
0.8002606
|
0.7595456
|
0.7195867
|
0.6804722
|
0.6422871
|
0.6051133
|
0.5690299
|
0.5341132
|
0.5004371
|
0.4680730
|
0.4370904
|
0.4075571
|
0.3795394
|
0.3531023
|
0.3283101
|
0.3052263
|
0.2839144
|
0.2644380
|
0.2468613
|
0.2312493
|
0.2176684
|
0.2061868
|
0.1968749
|
0.1898057
|
0.1850556
|
0.1827045
|
0.1828366
|
0.1855408
|
0.1909115
|
0.1990492
|
0.2100609
|
0.2240610
|
0.2411722
|
0.2615257
|
0.2852627
|
0.3125296
|
0.3432556
|
0.3770633
|
0.4135452
|
0.4522817
|
0.4928392
|
0.5347675
|
0.5775981
|
0.6208438
|
0.6639974
|
0.7065323
|
0.7479030
|
0.7875467
|
0.8248846
|
0.8593250
|
0.8902662
|
0.9171003
|
0.9392180
|
0.9560130
|
0.9668884
|
0.9712624
|
0.9685756
|
0.9582982
|
0.9399377
|
0.9130479
|
0.8772369
|
0.8321769
|
0.7776130
|
0.7133732
|
0.6393768
|
0.5556445
|
0.4624081
|
0.3605498
|
0.2511832
|
0.1354407
|
0.0144603
|
-0.1106290
|
-0.2387202
|
-0.3687412
|
-0.4996663
|
-0.6305273
|
-0.7604230
|
-0.8885268
|
-1.0140931
|
-1.1364623
|
-1.2550630
|
-1.3694134
|
-1.4791204
|
-1.583877
|
-1.683458
|
-1.777718
|
-1.866579
|
-1.950031
|
-2.028119
|
-2.100938
|
-2.168626
|
-2.231354
|
-2.289322
|
-2.342750
|
-2.391872
|
-2.436934
|
-2.478184
|
|
Sox9
|
0.6459327
|
0.6194119
|
0.5930953
|
0.5670639
|
0.5413977
|
0.5161748
|
0.4914719
|
0.4673646
|
0.4439265
|
0.4212305
|
0.3993479
|
0.3783490
|
0.3583030
|
0.3392784
|
0.3213427
|
0.3045630
|
0.2890059
|
0.2747378
|
0.2618250
|
0.2503341
|
0.2403319
|
0.2318861
|
0.2250649
|
0.2199381
|
0.2165765
|
0.2150529
|
0.2154420
|
0.2178208
|
0.2222690
|
0.2288691
|
0.2377071
|
0.2488726
|
0.2624591
|
0.2785645
|
0.2972915
|
0.3187476
|
0.3430461
|
0.3703059
|
0.4006468
|
0.4339781
|
0.4699143
|
0.5080399
|
0.5479286
|
0.5891417
|
0.6312268
|
0.6737182
|
0.7161360
|
0.7579869
|
0.7987649
|
0.8379520
|
0.8750203
|
0.9094329
|
0.9406468
|
0.9681147
|
0.9912879
|
1.0096193
|
1.0225666
|
1.0295959
|
1.0301854
|
1.0238306
|
1.0100480
|
0.9883813
|
0.9584069
|
0.9197404
|
0.8720443
|
0.8150357
|
0.7484955
|
0.6722785
|
0.5863243
|
0.4907677
|
0.3863716
|
0.2741395
|
0.1551205
|
0.0304019
|
-0.0988997
|
-0.2316489
|
-0.3667031
|
-0.5029268
|
-0.6392058
|
-0.7744635
|
-0.9076777
|
-1.0378964
|
-1.1642534
|
-1.2859820
|
-1.4024264
|
-1.5130495
|
-1.617437
|
-1.715299
|
-1.806465
|
-1.890879
|
-1.968587
|
-2.039727
|
-2.104515
|
-2.163228
|
-2.216191
|
-2.263765
|
-2.306330
|
-2.344276
|
-2.377994
|
-2.407866
|
|
Foxg1
|
0.5488428
|
0.5249359
|
0.5012581
|
0.4778899
|
0.4549098
|
0.4323941
|
0.4104175
|
0.3890529
|
0.3683716
|
0.3484432
|
0.3293363
|
0.3111178
|
0.2938541
|
0.2776103
|
0.2624512
|
0.2484408
|
0.2356432
|
0.2241225
|
0.2139430
|
0.2051695
|
0.1978678
|
0.1921048
|
0.1879489
|
0.1854703
|
0.1847413
|
0.1858369
|
0.1888350
|
0.1938167
|
0.2008671
|
0.2100754
|
0.2215358
|
0.2353476
|
0.2516159
|
0.2704524
|
0.2919758
|
0.3163125
|
0.3435972
|
0.3739741
|
0.4075916
|
0.4443809
|
0.4839629
|
0.5259231
|
0.5698300
|
0.6152329
|
0.6616595
|
0.7086150
|
0.7555811
|
0.8020165
|
0.8473568
|
0.8910163
|
0.9323900
|
0.9708561
|
1.0057799
|
1.0365180
|
1.0624232
|
1.0828507
|
1.0971639
|
1.1047426
|
1.1049901
|
1.0973423
|
1.0812764
|
1.0563207
|
1.0220644
|
0.9781680
|
0.9243732
|
0.8605137
|
0.7865246
|
0.7024521
|
0.6084617
|
0.5049501
|
0.3929901
|
0.2738853
|
0.1489467
|
0.0194743
|
-0.1132604
|
-0.2480308
|
-0.3836700
|
-0.5190840
|
-0.6532630
|
-0.7852902
|
-0.9143489
|
-1.0397267
|
-1.1608175
|
-1.2771212
|
-1.3882418
|
-1.4938825
|
-1.593840
|
-1.687998
|
-1.776319
|
-1.858832
|
-1.935630
|
-2.006855
|
-2.072691
|
-2.133356
|
-2.189094
|
-2.240165
|
-2.286843
|
-2.329407
|
-2.368135
|
-2.403304
|
|
Creb5
|
0.8664662
|
0.8370160
|
0.8078765
|
0.7791239
|
0.7508317
|
0.7230713
|
0.6959118
|
0.6694200
|
0.6436605
|
0.6186963
|
0.5945881
|
0.5713955
|
0.5491762
|
0.5279867
|
0.5078826
|
0.4889184
|
0.4711482
|
0.4546253
|
0.4394031
|
0.4255350
|
0.4130749
|
0.4020771
|
0.3925970
|
0.3846912
|
0.3784178
|
0.3738372
|
0.3710115
|
0.3700061
|
0.3708889
|
0.3737316
|
0.3786098
|
0.3856036
|
0.3947976
|
0.4062823
|
0.4201539
|
0.4365151
|
0.4554759
|
0.4771541
|
0.5016707
|
0.5289231
|
0.5584929
|
0.5899270
|
0.6227567
|
0.6564952
|
0.6906361
|
0.7246528
|
0.7579983
|
0.7901063
|
0.8203926
|
0.8482578
|
0.8730903
|
0.8942714
|
0.9111796
|
0.9231973
|
0.9297173
|
0.9301509
|
0.9239361
|
0.9105471
|
0.8895040
|
0.8603835
|
0.8228293
|
0.7765631
|
0.7213962
|
0.6572393
|
0.5841136
|
0.5021593
|
0.4116439
|
0.3129680
|
0.2066690
|
0.0935159
|
-0.0251140
|
-0.1476723
|
-0.2726558
|
-0.3986317
|
-0.5242608
|
-0.6483161
|
-0.7696988
|
-0.8874497
|
-1.0007561
|
-1.1089542
|
-1.2115285
|
-1.3081052
|
-1.3984448
|
-1.4824301
|
-1.5600530
|
-1.6314004
|
-1.696639
|
-1.755999
|
-1.809763
|
-1.858247
|
-1.901795
|
-1.940763
|
-1.975510
|
-2.006395
|
-2.033764
|
-2.057953
|
-2.079278
|
-2.098035
|
-2.114501
|
-2.128929
|
|
Sox11
|
0.7697327
|
0.7554836
|
0.7412900
|
0.7271861
|
0.7132062
|
0.6993840
|
0.6857533
|
0.6723477
|
0.6592004
|
0.6463446
|
0.6338133
|
0.6216393
|
0.6098552
|
0.5984935
|
0.5875866
|
0.5771668
|
0.5672662
|
0.5579169
|
0.5491511
|
0.5410006
|
0.5334975
|
0.5266737
|
0.5205614
|
0.5151927
|
0.5105997
|
0.5068148
|
0.5038705
|
0.5017995
|
0.5006347
|
0.5004092
|
0.5011567
|
0.5029107
|
0.5057056
|
0.5095760
|
0.5145568
|
0.5206837
|
0.5279927
|
0.5365204
|
0.5463014
|
0.5572512
|
0.5691241
|
0.5816618
|
0.5946045
|
0.6076912
|
0.6206592
|
0.6332444
|
0.6451814
|
0.6562033
|
0.6660423
|
0.6744299
|
0.6810974
|
0.6857760
|
0.6881978
|
0.6880958
|
0.6852053
|
0.6792641
|
0.6700134
|
0.6571990
|
0.6405722
|
0.6198907
|
0.5949205
|
0.5654364
|
0.5312243
|
0.4920826
|
0.4478243
|
0.3982787
|
0.3432942
|
0.2827406
|
0.2165122
|
0.1445851
|
0.0672588
|
-0.0150508
|
-0.1019157
|
-0.1928967
|
-0.2875452
|
-0.3854045
|
-0.4860118
|
-0.5889001
|
-0.6936002
|
-0.7996437
|
-0.9065654
|
-1.0139062
|
-1.1212165
|
-1.2280593
|
-1.3340133
|
-1.4386769
|
-1.541671
|
-1.642641
|
-1.741264
|
-1.837243
|
-1.930320
|
-2.020266
|
-2.106892
|
-2.190042
|
-2.269598
|
-2.345476
|
-2.417625
|
-2.486028
|
-2.550697
|
-2.611669
|
|
Pbx1
|
0.3947038
|
0.3965766
|
0.3984693
|
0.4004012
|
0.4023918
|
0.4044606
|
0.4066268
|
0.4089101
|
0.4113299
|
0.4139058
|
0.4166573
|
0.4196042
|
0.4227660
|
0.4261627
|
0.4298139
|
0.4337397
|
0.4379599
|
0.4424946
|
0.4473641
|
0.4525887
|
0.4581886
|
0.4641846
|
0.4705972
|
0.4774473
|
0.4847560
|
0.4925444
|
0.5008340
|
0.5096463
|
0.5190033
|
0.5289270
|
0.5394397
|
0.5505641
|
0.5623231
|
0.5747401
|
0.5878384
|
0.6016421
|
0.6161755
|
0.6314633
|
0.6475280
|
0.6642797
|
0.6814753
|
0.6988585
|
0.7161702
|
0.7331487
|
0.7495298
|
0.7650469
|
0.7794314
|
0.7924129
|
0.8037199
|
0.8130804
|
0.8202225
|
0.8248751
|
0.8267689
|
0.8256375
|
0.8212181
|
0.8132531
|
0.8014913
|
0.7856891
|
0.7656121
|
0.7410368
|
0.7117521
|
0.6775614
|
0.6382842
|
0.5937584
|
0.5438425
|
0.4884173
|
0.4273888
|
0.3606906
|
0.2882858
|
0.2102245
|
0.1268822
|
0.0387470
|
-0.0536864
|
-0.1499198
|
-0.2494546
|
-0.3517940
|
-0.4564464
|
-0.5629278
|
-0.6707648
|
-0.7794969
|
-0.8886795
|
-0.9978858
|
-1.1067095
|
-1.2147668
|
-1.3216979
|
-1.4271687
|
-1.530873
|
-1.632530
|
-1.731892
|
-1.828736
|
-1.922870
|
-2.014132
|
-2.102386
|
-2.187523
|
-2.269462
|
-2.348147
|
-2.423544
|
-2.495640
|
-2.564445
|
-2.629983
|
|
Pou3f3
|
0.5897745
|
0.5819481
|
0.5741688
|
0.5664706
|
0.5588872
|
0.5514522
|
0.5441989
|
0.5371603
|
0.5303696
|
0.5238593
|
0.5176622
|
0.5118108
|
0.5063375
|
0.5012745
|
0.4966543
|
0.4925091
|
0.4888711
|
0.4857727
|
0.4832464
|
0.4813247
|
0.4800403
|
0.4794263
|
0.4795158
|
0.4803425
|
0.4819401
|
0.4843431
|
0.4875863
|
0.4917050
|
0.4967354
|
0.5027139
|
0.5096781
|
0.5176661
|
0.5267171
|
0.5368712
|
0.5481695
|
0.5606542
|
0.5743689
|
0.5893584
|
0.6056655
|
0.6231919
|
0.6416449
|
0.6607140
|
0.6800841
|
0.6994349
|
0.7184411
|
0.7367725
|
0.7540943
|
0.7700677
|
0.7843508
|
0.7965995
|
0.8064689
|
0.8136145
|
0.8176941
|
0.8183696
|
0.8153090
|
0.8081890
|
0.7966971
|
0.7805348
|
0.7594199
|
0.7330901
|
0.7013061
|
0.6638547
|
0.6205527
|
0.5712502
|
0.5158346
|
0.4542338
|
0.3864201
|
0.3124140
|
0.2322870
|
0.1462285
|
0.0548186
|
-0.0412318
|
-0.1412103
|
-0.2444091
|
-0.3501317
|
-0.4576984
|
-0.5664520
|
-0.6757631
|
-0.7850345
|
-0.8937060
|
-1.0012570
|
-1.1072104
|
-1.2111343
|
-1.3126436
|
-1.4114010
|
-1.5071168
|
-1.599549
|
-1.688500
|
-1.773819
|
-1.855395
|
-1.933158
|
-2.007072
|
-2.077137
|
-2.143380
|
-2.205857
|
-2.264643
|
-2.319836
|
-2.371547
|
-2.419903
|
-2.465037
|
|
Pou3f2
|
0.4879578
|
0.4873613
|
0.4867886
|
0.4862634
|
0.4858094
|
0.4854502
|
0.4852095
|
0.4851110
|
0.4851784
|
0.4854354
|
0.4859056
|
0.4866130
|
0.4875812
|
0.4888344
|
0.4903964
|
0.4922913
|
0.4945435
|
0.4971773
|
0.5002173
|
0.5036883
|
0.5076152
|
0.5120233
|
0.5169381
|
0.5223855
|
0.5283917
|
0.5349832
|
0.5421869
|
0.5500304
|
0.5585416
|
0.5677488
|
0.5776812
|
0.5883683
|
0.5998406
|
0.6121290
|
0.6252654
|
0.6392823
|
0.6542132
|
0.6700927
|
0.6869526
|
0.7046823
|
0.7229738
|
0.7415003
|
0.7599292
|
0.7779219
|
0.7951344
|
0.8112175
|
0.8258181
|
0.8385794
|
0.8491431
|
0.8571507
|
0.8622451
|
0.8640731
|
0.8622877
|
0.8565509
|
0.8465365
|
0.8319331
|
0.8124481
|
0.7878104
|
0.7577752
|
0.7221272
|
0.6806847
|
0.6333043
|
0.5798843
|
0.5203695
|
0.4547544
|
0.3830879
|
0.3054758
|
0.2220845
|
0.1331430
|
0.0390073
|
-0.0595776
|
-0.1617469
|
-0.2666489
|
-0.3734544
|
-0.4813647
|
-0.5896204
|
-0.6975075
|
-0.8043643
|
-0.9095859
|
-1.0126283
|
-1.1130106
|
-1.2103171
|
-1.3041968
|
-1.3943632
|
-1.4805918
|
-1.5627176
|
-1.640631
|
-1.714275
|
-1.783637
|
-1.848749
|
-1.909677
|
-1.966519
|
-2.019400
|
-2.068465
|
-2.113875
|
-2.155806
|
-2.194438
|
-2.229960
|
-2.262561
|
-2.292428
|
|
Meis2
|
-0.0785949
|
-0.0623705
|
-0.0460733
|
-0.0296910
|
-0.0132108
|
0.0033801
|
0.0200947
|
0.0369462
|
0.0539480
|
0.0711136
|
0.0884569
|
0.1059918
|
0.1237324
|
0.1416932
|
0.1598886
|
0.1783334
|
0.1970426
|
0.2160315
|
0.2353153
|
0.2549098
|
0.2748309
|
0.2950946
|
0.3157173
|
0.3367156
|
0.3581063
|
0.3799066
|
0.4021339
|
0.4248059
|
0.4479404
|
0.4715557
|
0.4956704
|
0.5203033
|
0.5454736
|
0.5712008
|
0.5975045
|
0.6244052
|
0.6519231
|
0.6800792
|
0.7088919
|
0.7382557
|
0.7678948
|
0.7975160
|
0.8268206
|
0.8555043
|
0.8832579
|
0.9097672
|
0.9347142
|
0.9577776
|
0.9786332
|
0.9969555
|
1.0124187
|
1.0246973
|
1.0334684
|
1.0384123
|
1.0392149
|
1.0355690
|
1.0271762
|
1.0137493
|
0.9950141
|
0.9707122
|
0.9406034
|
0.9044685
|
0.8621119
|
0.8133656
|
0.7580916
|
0.6961863
|
0.6275834
|
0.5522586
|
0.4702331
|
0.3816414
|
0.2870082
|
0.1869966
|
0.0822827
|
-0.0264492
|
-0.1385119
|
-0.2532194
|
-0.3698927
|
-0.4878648
|
-0.6064860
|
-0.7251296
|
-0.8431964
|
-0.9601201
|
-1.0753718
|
-1.1884640
|
-1.2989537
|
-1.4064461
|
-1.510595
|
-1.611107
|
-1.707737
|
-1.800293
|
-1.888631
|
-1.972655
|
-2.052312
|
-2.127591
|
-2.198520
|
-2.265159
|
-2.327597
|
-2.385949
|
-2.440350
|
-2.490953
|
|
Tshz2
|
0.0416828
|
0.0656549
|
0.0897702
|
0.1140113
|
0.1383603
|
0.1627991
|
0.1873087
|
0.2118700
|
0.2364633
|
0.2610682
|
0.2856642
|
0.3102300
|
0.3347440
|
0.3591843
|
0.3835281
|
0.4077526
|
0.4318344
|
0.4557495
|
0.4794738
|
0.5029825
|
0.5262507
|
0.5492529
|
0.5719633
|
0.5943558
|
0.6164041
|
0.6380813
|
0.6593605
|
0.6802143
|
0.7006154
|
0.7205359
|
0.7399480
|
0.7588236
|
0.7771346
|
0.7948527
|
0.8119495
|
0.8283966
|
0.8441658
|
0.8592286
|
0.8735550
|
0.8870430
|
0.8994921
|
0.9106932
|
0.9204367
|
0.9285123
|
0.9347100
|
0.9388209
|
0.9406379
|
0.9399568
|
0.9365768
|
0.9303022
|
0.9209433
|
0.9083173
|
0.8922502
|
0.8725777
|
0.8491467
|
0.8218168
|
0.7904618
|
0.7549714
|
0.7152524
|
0.6712305
|
0.6228518
|
0.5700844
|
0.5129198
|
0.4513741
|
0.3854899
|
0.3153368
|
0.2410131
|
0.1626458
|
0.0803924
|
-0.0055191
|
-0.0946170
|
-0.1863561
|
-0.2802013
|
-0.3756316
|
-0.4721438
|
-0.5692553
|
-0.6665077
|
-0.7634687
|
-0.8597349
|
-0.9549332
|
-1.0487220
|
-1.1407925
|
-1.2308688
|
-1.3187085
|
-1.4041017
|
-1.4868710
|
-1.566870
|
-1.643982
|
-1.718121
|
-1.789223
|
-1.857254
|
-1.922199
|
-1.984066
|
-2.042881
|
-2.098686
|
-2.151538
|
-2.201505
|
-2.248668
|
-2.293114
|
-2.334938
|
|
Npas3
|
0.0095120
|
0.0354918
|
0.0615956
|
0.0878013
|
0.1140868
|
0.1404291
|
0.1668049
|
0.1931903
|
0.2195612
|
0.2458927
|
0.2721596
|
0.2983363
|
0.3243967
|
0.3503141
|
0.3760616
|
0.4016118
|
0.4269369
|
0.4520087
|
0.4767987
|
0.5012780
|
0.5254174
|
0.5491873
|
0.5725578
|
0.5954989
|
0.6179801
|
0.6399710
|
0.6614406
|
0.6823581
|
0.7026922
|
0.7224117
|
0.7414852
|
0.7598815
|
0.7775688
|
0.7945159
|
0.8106913
|
0.8260635
|
0.8406013
|
0.8542736
|
0.8670480
|
0.8788378
|
0.8894825
|
0.8988155
|
0.9066702
|
0.9128805
|
0.9172803
|
0.9197049
|
0.9199911
|
0.9179777
|
0.9135060
|
0.9064205
|
0.8965698
|
0.8838066
|
0.8679893
|
0.8489820
|
0.8266559
|
0.8008896
|
0.7715706
|
0.7385957
|
0.7018721
|
0.6613187
|
0.6168666
|
0.5684607
|
0.5160603
|
0.4596406
|
0.3991932
|
0.3347281
|
0.2662738
|
0.1938788
|
0.1176129
|
0.0376031
|
-0.0458110
|
-0.1322201
|
-0.2212162
|
-0.3123948
|
-0.4053568
|
-0.4997112
|
-0.5950764
|
-0.6910828
|
-0.7873743
|
-0.8836100
|
-0.9794659
|
-1.0746363
|
-1.1688348
|
-1.2617956
|
-1.3532742
|
-1.4430478
|
-1.530916
|
-1.616701
|
-1.700247
|
-1.781420
|
-1.860108
|
-1.936220
|
-2.009685
|
-2.080452
|
-2.148485
|
-2.213768
|
-2.276299
|
-2.336092
|
-2.393171
|
-2.447575
|
|
Etv5
|
1.6120800
|
1.5011475
|
1.3930841
|
1.2880615
|
1.1862298
|
1.0877179
|
0.9926351
|
0.9010723
|
0.8131036
|
0.7287873
|
0.6481681
|
0.5712780
|
0.4981385
|
0.4287618
|
0.3631524
|
0.3013089
|
0.2432253
|
0.1888929
|
0.1383014
|
0.0914407
|
0.0483024
|
0.0088809
|
-0.0268246
|
-0.0588088
|
-0.0870592
|
-0.1115540
|
-0.1322608
|
-0.1491348
|
-0.1621175
|
-0.1711342
|
-0.1760926
|
-0.1768804
|
-0.1733629
|
-0.1653805
|
-0.1527460
|
-0.1352414
|
-0.1126140
|
-0.0845732
|
-0.0507928
|
-0.0112129
|
0.0338239
|
0.0839368
|
0.1387241
|
0.1977534
|
0.2605520
|
0.3265983
|
0.3953148
|
0.4660621
|
0.5381341
|
0.6107559
|
0.6830822
|
0.7541987
|
0.8231260
|
0.8888248
|
0.9502049
|
1.0061357
|
1.0554601
|
1.0970104
|
1.1296276
|
1.1521815
|
1.1635947
|
1.1628677
|
1.1491052
|
1.1215447
|
1.0795847
|
1.0228133
|
0.9510363
|
0.8643027
|
0.7629278
|
0.6476713
|
0.5204068
|
0.3834024
|
0.2389509
|
0.0893186
|
-0.0633023
|
-0.2168386
|
-0.3693745
|
-0.5191832
|
-0.6647520
|
-0.8047982
|
-0.9382768
|
-1.0643805
|
-1.1825316
|
-1.2923677
|
-1.3937224
|
-1.4866018
|
-1.571159
|
-1.647669
|
-1.716500
|
-1.778091
|
-1.832929
|
-1.881528
|
-1.924415
|
-1.962111
|
-1.995126
|
-2.023945
|
-2.049027
|
-2.070798
|
-2.089649
|
-2.105938
|
heatmap_matrix_q_value_5_10_minus_5 <- left_join(select(transcription_factors_table_q_value_5_10_minus_5, gene, pval, qval, num_cells_expressed), heatmap_matrix_q_value_5_10_minus_5)
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=TRUE, return_matrix = TRUE)

ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_5_10_minus_5, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "3_forebrain_oligodendrocytes_joint_forebrain_differential_gene_test_analysis_qval_5_10_minus_5_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes: 3288
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 175
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf
## 2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
|
gene
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
16
|
17
|
18
|
19
|
20
|
21
|
22
|
23
|
24
|
25
|
26
|
27
|
28
|
29
|
30
|
31
|
32
|
33
|
34
|
35
|
36
|
37
|
38
|
39
|
40
|
41
|
42
|
43
|
44
|
45
|
46
|
47
|
48
|
49
|
50
|
51
|
52
|
53
|
54
|
55
|
56
|
57
|
58
|
59
|
60
|
61
|
62
|
63
|
64
|
65
|
66
|
67
|
68
|
69
|
70
|
71
|
72
|
73
|
74
|
75
|
76
|
77
|
78
|
79
|
80
|
81
|
82
|
83
|
84
|
85
|
86
|
87
|
88
|
89
|
90
|
91
|
92
|
93
|
94
|
95
|
96
|
97
|
98
|
99
|
100
|
|
Gabpb2
|
3.000000
|
3.000000
|
3.000000
|
2.759125
|
2.506764
|
2.266213
|
2.037274
|
1.819712
|
1.613266
|
1.4176494
|
1.2325557
|
1.0576657
|
0.8926500
|
0.7371730
|
0.5908970
|
0.4534850
|
0.3246039
|
0.2039268
|
0.0911356
|
-0.0140775
|
-0.1120078
|
-0.2029366
|
-0.2871300
|
-0.3648378
|
-0.4362919
|
-0.5017061
|
-0.5612743
|
-0.6151702
|
-0.6635461
|
-0.7065322
|
-0.7442354
|
-0.7767381
|
-0.8040973
|
-0.8263430
|
-0.8434762
|
-0.8554677
|
-0.8622554
|
-0.8637417
|
-0.8597954
|
-0.8504502
|
-0.8359812
|
-0.8166543
|
-0.7927143
|
-0.7643914
|
-0.7319077
|
-0.6954829
|
-0.6553401
|
-0.6117111
|
-0.5648411
|
-0.5149938
|
-0.4624555
|
-0.4075397
|
-0.3505905
|
-0.2919863
|
-0.2321422
|
-0.1715125
|
-0.1105923
|
-0.0499181
|
0.0099325
|
0.0683421
|
0.1246556
|
0.1781841
|
0.2282100
|
0.2739928
|
0.3147775
|
0.3498033
|
0.3783143
|
0.3995711
|
0.4128641
|
0.4176296
|
0.4139237
|
0.4020545
|
0.3823845
|
0.3553235
|
0.3213215
|
0.2808605
|
0.2344480
|
0.1826092
|
0.1258808
|
0.0648040
|
-0.0000808
|
-0.0682403
|
-0.1391523
|
-0.2123107
|
-0.2872290
|
-0.3634434
|
-0.4405155
|
-0.5180345
|
-0.5956182
|
-0.6729144
|
-0.7496012
|
-0.8253874
|
-0.9000116
|
-0.9732425
|
-1.0448768
|
-1.1147393
|
-1.1826805
|
-1.2485757
|
-1.3123231
|
-1.3738422
|
|
Ssrp1
|
2.989236
|
2.829115
|
2.670522
|
2.513668
|
2.358756
|
2.205980
|
2.055528
|
1.907580
|
1.762312
|
1.6198909
|
1.4804765
|
1.3442239
|
1.2112815
|
1.0817923
|
0.9558937
|
0.8337183
|
0.7153936
|
0.6010433
|
0.4907869
|
0.3847404
|
0.2830170
|
0.1857272
|
0.0929797
|
0.0048814
|
-0.0784618
|
-0.1569443
|
-0.2304604
|
-0.2989039
|
-0.3621670
|
-0.4201403
|
-0.4727116
|
-0.5197656
|
-0.5611831
|
-0.5968403
|
-0.6266079
|
-0.6503508
|
-0.6679268
|
-0.6791862
|
-0.6839764
|
-0.6823806
|
-0.6748031
|
-0.6616643
|
-0.6433784
|
-0.6203558
|
-0.5930044
|
-0.5617312
|
-0.5269435
|
-0.4890505
|
-0.4484638
|
-0.4055989
|
-0.3608755
|
-0.3147186
|
-0.2675585
|
-0.2198317
|
-0.1719806
|
-0.1244542
|
-0.0777072
|
-0.0322006
|
0.0115993
|
0.0532208
|
0.0921883
|
0.1280221
|
0.1602402
|
0.1883592
|
0.2118951
|
0.2303653
|
0.2432900
|
0.2501937
|
0.2506072
|
0.2441520
|
0.2309104
|
0.2111267
|
0.1850536
|
0.1529504
|
0.1150825
|
0.0717200
|
0.0231373
|
-0.0303883
|
-0.0885771
|
-0.1511481
|
-0.2178195
|
-0.2883094
|
-0.3623371
|
-0.4396230
|
-0.5198897
|
-0.6028624
|
-0.6882696
|
-0.7758434
|
-0.8653202
|
-0.9564409
|
-1.0489517
|
-1.1426039
|
-1.2371545
|
-1.3323665
|
-1.4280092
|
-1.5238581
|
-1.6196952
|
-1.7153093
|
-1.8104958
|
-1.9050567
|
|
Cdc5l
|
2.831576
|
2.668810
|
2.508251
|
2.350116
|
2.194609
|
2.041924
|
1.892242
|
1.745735
|
1.602564
|
1.4628783
|
1.3268198
|
1.1945201
|
1.0661028
|
0.9416831
|
0.8213691
|
0.7052620
|
0.5934570
|
0.4860437
|
0.3831072
|
0.2847285
|
0.1909851
|
0.1019525
|
0.0177040
|
-0.0616879
|
-0.1361508
|
-0.2056115
|
-0.2699955
|
-0.3292257
|
-0.3832218
|
-0.4318991
|
-0.4751681
|
-0.5129330
|
-0.5450907
|
-0.5715304
|
-0.5921317
|
-0.6067641
|
-0.6152854
|
-0.6175410
|
-0.6133681
|
-0.6028476
|
-0.5863959
|
-0.5644445
|
-0.5374184
|
-0.5057385
|
-0.4698248
|
-0.4300988
|
-0.3869853
|
-0.3409146
|
-0.2923243
|
-0.2416603
|
-0.1893786
|
-0.1359457
|
-0.0818396
|
-0.0275503
|
0.0264205
|
0.0795590
|
0.1313401
|
0.1812277
|
0.2286761
|
0.2731311
|
0.3140316
|
0.3508112
|
0.3829011
|
0.4097319
|
0.4307365
|
0.4453537
|
0.4530309
|
0.4532282
|
0.4454219
|
0.4292052
|
0.4047185
|
0.3723002
|
0.3323054
|
0.2851032
|
0.2310747
|
0.1706102
|
0.1041076
|
0.0319698
|
-0.0453968
|
-0.1275849
|
-0.2141875
|
-0.3047999
|
-0.3990213
|
-0.4964565
|
-0.5967169
|
-0.6994220
|
-0.8042007
|
-0.9106921
|
-1.0185467
|
-1.1274270
|
-1.2370083
|
-1.3469792
|
-1.4570422
|
-1.5669142
|
-1.6763262
|
-1.7850241
|
-1.8927685
|
-1.9993342
|
-2.1045111
|
-2.2081028
|
|
E2f1
|
2.456768
|
2.306685
|
2.161761
|
2.022044
|
1.887562
|
1.758316
|
1.634293
|
1.515460
|
1.401769
|
1.2931630
|
1.1895702
|
1.0909123
|
0.9971034
|
0.9080525
|
0.8236646
|
0.7438424
|
0.6684878
|
0.5975028
|
0.5307908
|
0.4682580
|
0.4098137
|
0.3553723
|
0.3048531
|
0.2581821
|
0.2152923
|
0.1761248
|
0.1406294
|
0.1087656
|
0.0805036
|
0.0558250
|
0.0347238
|
0.0172074
|
0.0032979
|
-0.0069666
|
-0.0135311
|
-0.0163216
|
-0.0152433
|
-0.0101793
|
-0.0009929
|
0.0122450
|
0.0291662
|
0.0493861
|
0.0725193
|
0.0981726
|
0.1259389
|
0.1553930
|
0.1860866
|
0.2175456
|
0.2492679
|
0.2807217
|
0.3113461
|
0.3405525
|
0.3677269
|
0.3922348
|
0.4134268
|
0.4306464
|
0.4432390
|
0.4505626
|
0.4520004
|
0.4469736
|
0.4349564
|
0.4154906
|
0.3882007
|
0.3528087
|
0.3091483
|
0.2571766
|
0.1969846
|
0.1288045
|
0.0530131
|
-0.0297745
|
-0.1183344
|
-0.2112710
|
-0.3072349
|
-0.4049484
|
-0.5032264
|
-0.6009924
|
-0.6972900
|
-0.7912888
|
-0.8822873
|
-0.9697111
|
-1.0531087
|
-1.1321438
|
-1.2065870
|
-1.2763049
|
-1.3412488
|
-1.4014433
|
-1.4569749
|
-1.5079804
|
-1.5546370
|
-1.5971519
|
-1.6357546
|
-1.6706884
|
-1.7022040
|
-1.7305545
|
-1.7559899
|
-1.7787543
|
-1.7990825
|
-1.8171979
|
-1.8333114
|
-1.8476202
|
|
Nr2e1
|
1.878116
|
1.789917
|
1.703342
|
1.618498
|
1.535485
|
1.454392
|
1.375303
|
1.298292
|
1.223426
|
1.1507672
|
1.0803696
|
1.0122825
|
0.9465500
|
0.8832112
|
0.8223012
|
0.7638516
|
0.7078905
|
0.6544438
|
0.6035351
|
0.5551864
|
0.5094188
|
0.4662529
|
0.4257092
|
0.3878087
|
0.3525736
|
0.3200277
|
0.2901968
|
0.2631096
|
0.2387979
|
0.2172976
|
0.1986487
|
0.1828967
|
0.1700925
|
0.1602936
|
0.1535648
|
0.1499786
|
0.1496163
|
0.1525691
|
0.1589338
|
0.1686224
|
0.1812888
|
0.1965715
|
0.2141081
|
0.2335330
|
0.2544747
|
0.2765539
|
0.2993818
|
0.3225591
|
0.3456752
|
0.3683083
|
0.3900256
|
0.4103843
|
0.4289329
|
0.4452134
|
0.4587638
|
0.4691213
|
0.4758262
|
0.4784258
|
0.4764798
|
0.4695650
|
0.4572814
|
0.4392584
|
0.4151611
|
0.3846964
|
0.3476205
|
0.3037447
|
0.2529421
|
0.1951534
|
0.1303920
|
0.0588267
|
-0.0188878
|
-0.1019332
|
-0.1894895
|
-0.2807456
|
-0.3749092
|
-0.4712148
|
-0.5689318
|
-0.6673707
|
-0.7658882
|
-0.8638915
|
-0.9608411
|
-1.0562527
|
-1.1496981
|
-1.2408052
|
-1.3292566
|
-1.4147884
|
-1.4971875
|
-1.5762888
|
-1.6519722
|
-1.7241586
|
-1.7928062
|
-1.8579070
|
-1.9194824
|
-1.9775798
|
-2.0322683
|
-2.0836360
|
-2.1317860
|
-2.1768333
|
-2.2189025
|
-2.2581248
|
|
Smarcc1
|
1.980831
|
1.886948
|
1.793804
|
1.701538
|
1.610288
|
1.520186
|
1.431364
|
1.343946
|
1.258056
|
1.1738123
|
1.0913316
|
1.0107264
|
0.9321062
|
0.8555779
|
0.7812455
|
0.7092104
|
0.6395719
|
0.5724270
|
0.5078707
|
0.4459967
|
0.3868969
|
0.3306623
|
0.2773830
|
0.2271487
|
0.1800486
|
0.1361722
|
0.0956094
|
0.0584508
|
0.0247883
|
-0.0052847
|
-0.0316731
|
-0.0542793
|
-0.0730029
|
-0.0877404
|
-0.0983847
|
-0.1048246
|
-0.1069443
|
-0.1046231
|
-0.0977396
|
-0.0863791
|
-0.0709098
|
-0.0517172
|
-0.0291857
|
-0.0036999
|
0.0243545
|
0.0545896
|
0.0866143
|
0.1200337
|
0.1544486
|
0.1894550
|
0.2246437
|
0.2596007
|
0.2939066
|
0.3271373
|
0.3588640
|
0.3886541
|
0.4160712
|
0.4406768
|
0.4620304
|
0.4796913
|
0.4932192
|
0.5021763
|
0.5061283
|
0.5046465
|
0.4973095
|
0.4837051
|
0.4634327
|
0.4361055
|
0.4013530
|
0.3589047
|
0.3089514
|
0.2518468
|
0.1879541
|
0.1176447
|
0.0412961
|
-0.0407097
|
-0.1279873
|
-0.2201496
|
-0.3168091
|
-0.4175796
|
-0.5220771
|
-0.6299211
|
-0.7407360
|
-0.8541523
|
-0.9698073
|
-1.0873463
|
-1.2064237
|
-1.3267036
|
-1.4478608
|
-1.5695814
|
-1.6915634
|
-1.8135174
|
-1.9351667
|
-2.0562483
|
-2.1765125
|
-2.2957237
|
-2.4136600
|
-2.5301137
|
-2.6448910
|
-2.7578117
|
|
Arid4a
|
1.515844
|
1.449813
|
1.384404
|
1.319722
|
1.255870
|
1.192945
|
1.131043
|
1.070256
|
1.010673
|
0.9523803
|
0.8954619
|
0.8399983
|
0.7860682
|
0.7337477
|
0.6831110
|
0.6342305
|
0.5871766
|
0.5420187
|
0.4988245
|
0.4576610
|
0.4185944
|
0.3816902
|
0.3470139
|
0.3146308
|
0.2846065
|
0.2570074
|
0.2319004
|
0.2093539
|
0.1894377
|
0.1722233
|
0.1577846
|
0.1461978
|
0.1375421
|
0.1319000
|
0.1293577
|
0.1300054
|
0.1339379
|
0.1412551
|
0.1520577
|
0.1662634
|
0.1835378
|
0.2035291
|
0.2258848
|
0.2502500
|
0.2762664
|
0.3035713
|
0.3317968
|
0.3605692
|
0.3895086
|
0.4182287
|
0.4463372
|
0.4734352
|
0.4991188
|
0.5229788
|
0.5446022
|
0.5635732
|
0.5794744
|
0.5918888
|
0.6004013
|
0.6046006
|
0.6040821
|
0.5984497
|
0.5873189
|
0.5703195
|
0.5470985
|
0.5173238
|
0.4806869
|
0.4369066
|
0.3857327
|
0.3270263
|
0.2611006
|
0.1884288
|
0.1094951
|
0.0247913
|
-0.0651866
|
-0.1599414
|
-0.2589778
|
-0.3618052
|
-0.4679401
|
-0.5769088
|
-0.6882494
|
-0.8015139
|
-0.9162699
|
-1.0321025
|
-1.1486150
|
-1.2654309
|
-1.3821940
|
-1.4985698
|
-1.6142454
|
-1.7289305
|
-1.8423569
|
-1.9542787
|
-2.0644722
|
-2.1727353
|
-2.2788874
|
-2.3827683
|
-2.4842376
|
-2.5831743
|
-2.6794752
|
-2.7730544
|
|
Pou6f1
|
2.694772
|
2.490870
|
2.294437
|
2.105546
|
1.924230
|
1.750490
|
1.584292
|
1.425576
|
1.274259
|
1.1302342
|
0.9933817
|
0.8635656
|
0.7406395
|
0.6244491
|
0.5148345
|
0.4116330
|
0.3146808
|
0.2238158
|
0.1388789
|
0.0597162
|
-0.0138197
|
-0.0818677
|
-0.1445574
|
-0.2020070
|
-0.2543225
|
-0.3015958
|
-0.3439042
|
-0.3813084
|
-0.4138512
|
-0.4415563
|
-0.4644262
|
-0.4824410
|
-0.4955561
|
-0.5037001
|
-0.5067722
|
-0.5046396
|
-0.4971342
|
-0.4840488
|
-0.4651391
|
-0.4403794
|
-0.4100691
|
-0.3745170
|
-0.3340263
|
-0.2889025
|
-0.2394627
|
-0.1860425
|
-0.1290042
|
-0.0687427
|
-0.0056928
|
0.0596659
|
0.1268038
|
0.1951375
|
0.2640271
|
0.3327742
|
0.4006224
|
0.4667586
|
0.5303165
|
0.5903822
|
0.6460016
|
0.6961909
|
0.7399482
|
0.7762683
|
0.8041594
|
0.8226620
|
0.8308689
|
0.8279477
|
0.8131626
|
0.7858986
|
0.7456830
|
0.6923495
|
0.6266665
|
0.5497726
|
0.4628802
|
0.3672497
|
0.2641650
|
0.1549106
|
0.0407507
|
-0.0770894
|
-0.1974398
|
-0.3191992
|
-0.4413459
|
-0.5629462
|
-0.6831597
|
-0.8012428
|
-0.9165494
|
-1.0285301
|
-1.1367292
|
-1.2407808
|
-1.3404032
|
-1.4353926
|
-1.5256164
|
-1.6110060
|
-1.6915491
|
-1.7672827
|
-1.8382853
|
-1.9046710
|
-1.9665820
|
-2.0241833
|
-2.0776572
|
-2.1271982
|
|
Elf2
|
2.326083
|
2.221356
|
2.117630
|
2.015036
|
1.913696
|
1.813730
|
1.715252
|
1.618375
|
1.523203
|
1.4298414
|
1.3383875
|
1.2489370
|
1.1615819
|
1.0764108
|
0.9935095
|
0.9129605
|
0.8348441
|
0.7592380
|
0.6862178
|
0.6158572
|
0.5482283
|
0.4834016
|
0.4214469
|
0.3624328
|
0.3064276
|
0.2534992
|
0.2037159
|
0.1571460
|
0.1138587
|
0.0739245
|
0.0374150
|
0.0044036
|
-0.0250341
|
-0.0508198
|
-0.0728726
|
-0.0911080
|
-0.1054381
|
-0.1157706
|
-0.1220126
|
-0.1242437
|
-0.1227774
|
-0.1179396
|
-0.1100531
|
-0.0994383
|
-0.0864146
|
-0.0713013
|
-0.0544182
|
-0.0360863
|
-0.0166284
|
0.0036301
|
0.0243615
|
0.0452352
|
0.0659175
|
0.0860718
|
0.1053589
|
0.1234369
|
0.1399617
|
0.1545876
|
0.1669679
|
0.1767554
|
0.1836037
|
0.1871678
|
0.1871054
|
0.1830782
|
0.1747530
|
0.1618032
|
0.1439107
|
0.1207672
|
0.0920760
|
0.0576171
|
0.0175294
|
-0.0279228
|
-0.0784690
|
-0.1338339
|
-0.1937389
|
-0.2579025
|
-0.3260423
|
-0.3978754
|
-0.4731197
|
-0.5514948
|
-0.6327228
|
-0.7165293
|
-0.8026439
|
-0.8908011
|
-0.9807412
|
-1.0722102
|
-1.1649610
|
-1.2587537
|
-1.3533557
|
-1.4485425
|
-1.5440977
|
-1.6398134
|
-1.7354902
|
-1.8309375
|
-1.9259737
|
-2.0204258
|
-2.1141298
|
-2.2069306
|
-2.2986817
|
-2.3892450
|
|
Ybx1
|
2.236275
|
2.142877
|
2.049650
|
1.956717
|
1.864203
|
1.772230
|
1.680923
|
1.590403
|
1.500793
|
1.4122155
|
1.3247930
|
1.2386470
|
1.1538992
|
1.0706709
|
0.9890833
|
0.9092575
|
0.8313140
|
0.7553736
|
0.6815566
|
0.6099832
|
0.5407735
|
0.4740475
|
0.4099249
|
0.3485256
|
0.2899692
|
0.2343753
|
0.1818634
|
0.1325532
|
0.0865642
|
0.0440160
|
0.0050284
|
-0.0302788
|
-0.0617858
|
-0.0893724
|
-0.1129183
|
-0.1323032
|
-0.1474061
|
-0.1581061
|
-0.1642863
|
-0.1660197
|
-0.1636363
|
-0.1574839
|
-0.1479101
|
-0.1352624
|
-0.1198880
|
-0.1021344
|
-0.0823490
|
-0.0608791
|
-0.0380725
|
-0.0142768
|
0.0101600
|
0.0348897
|
0.0595640
|
0.0838343
|
0.1073519
|
0.1297677
|
0.1507326
|
0.1698974
|
0.1869126
|
0.2014287
|
0.2130963
|
0.2215659
|
0.2264881
|
0.2275139
|
0.2242942
|
0.2164805
|
0.2037247
|
0.1856792
|
0.1619970
|
0.1323972
|
0.0969565
|
0.0558735
|
0.0093473
|
-0.0424226
|
-0.0992364
|
-0.1608941
|
-0.2271955
|
-0.2979401
|
-0.3729276
|
-0.4519574
|
-0.5348290
|
-0.6213421
|
-0.7112963
|
-0.8044913
|
-0.9007274
|
-0.9998046
|
-1.1015235
|
-1.2056850
|
-1.3120902
|
-1.4205407
|
-1.5308384
|
-1.6427858
|
-1.7561858
|
-1.8708418
|
-1.9865578
|
-2.1031382
|
-2.2203882
|
-2.3381134
|
-2.4561203
|
-2.5742157
|
|
Hmgb3
|
2.484765
|
2.361251
|
2.238733
|
2.117402
|
1.997446
|
1.879045
|
1.762375
|
1.647605
|
1.534899
|
1.4244149
|
1.3163042
|
1.2107117
|
1.1077761
|
1.0076296
|
0.9103980
|
0.8162010
|
0.7251522
|
0.6373594
|
0.5529251
|
0.4719463
|
0.3945154
|
0.3207206
|
0.2506463
|
0.1843737
|
0.1219813
|
0.0635460
|
0.0091434
|
-0.0411514
|
-0.0872628
|
-0.1291139
|
-0.1666258
|
-0.1997166
|
-0.2283003
|
-0.2522862
|
-0.2715777
|
-0.2860713
|
-0.2956557
|
-0.3002109
|
-0.2996120
|
-0.2939440
|
-0.2835798
|
-0.2689060
|
-0.2503046
|
-0.2281552
|
-0.2028372
|
-0.1747311
|
-0.1442210
|
-0.1116951
|
-0.0775473
|
-0.0421779
|
-0.0059941
|
0.0305894
|
0.0671503
|
0.1032591
|
0.1384791
|
0.1723667
|
0.2044727
|
0.2343427
|
0.2615183
|
0.2855386
|
0.3059414
|
0.3222647
|
0.3340489
|
0.3408387
|
0.3421850
|
0.3376477
|
0.3267982
|
0.3092223
|
0.2845236
|
0.2524084
|
0.2130510
|
0.1667939
|
0.1139934
|
0.0550179
|
-0.0097534
|
-0.0799318
|
-0.1551210
|
-0.2349178
|
-0.3189145
|
-0.4066995
|
-0.4978594
|
-0.5919805
|
-0.6886505
|
-0.7874598
|
-0.8880040
|
-0.9898850
|
-1.0927132
|
-1.1961091
|
-1.2997053
|
-1.4031480
|
-1.5060990
|
-1.6082367
|
-1.7092583
|
-1.8088806
|
-1.9068411
|
-2.0028991
|
-2.0968364
|
-2.1884577
|
-2.2775908
|
-2.3640864
|
|
Zfp131
|
2.381023
|
2.257747
|
2.135936
|
2.015755
|
1.897363
|
1.780910
|
1.666541
|
1.554392
|
1.444593
|
1.3372688
|
1.2325369
|
1.1305096
|
1.0312936
|
0.9349909
|
0.8416986
|
0.7515097
|
0.6645133
|
0.5807953
|
0.5004385
|
0.4235232
|
0.3501278
|
0.2803290
|
0.2142026
|
0.1518237
|
0.0932675
|
0.0386098
|
-0.0120729
|
-0.0587021
|
-0.1011974
|
-0.1394755
|
-0.1734496
|
-0.2030290
|
-0.2281185
|
-0.2486171
|
-0.2644182
|
-0.2754080
|
-0.2814655
|
-0.2824611
|
-0.2782613
|
-0.2689497
|
-0.2549074
|
-0.2365315
|
-0.2142156
|
-0.1883517
|
-0.1593323
|
-0.1275519
|
-0.0934087
|
-0.0573055
|
-0.0196511
|
0.0191392
|
0.0586424
|
0.0984279
|
0.1380571
|
0.1770833
|
0.2150520
|
0.2515014
|
0.2859630
|
0.3179627
|
0.3470218
|
0.3726583
|
0.3943889
|
0.4117307
|
0.4242033
|
0.4313311
|
0.4326461
|
0.4276907
|
0.4160206
|
0.3972079
|
0.3708449
|
0.3366326
|
0.2947627
|
0.2456019
|
0.1895304
|
0.1269387
|
0.0582258
|
-0.0162035
|
-0.0959406
|
-0.1805751
|
-0.2696968
|
-0.3628978
|
-0.4597739
|
-0.5599264
|
-0.6629636
|
-0.7685022
|
-0.8761686
|
-0.9855996
|
-1.0964442
|
-1.2083637
|
-1.3210327
|
-1.4341401
|
-1.5473889
|
-1.6604971
|
-1.7731979
|
-1.8852395
|
-1.9963857
|
-2.1064153
|
-2.2151224
|
-2.3223160
|
-2.4278196
|
-2.5314710
|
|
Myef2
|
2.126145
|
2.071784
|
2.017625
|
1.963647
|
1.909831
|
1.856161
|
1.802617
|
1.749182
|
1.695839
|
1.6425702
|
1.5893603
|
1.5361929
|
1.4830523
|
1.4299234
|
1.3767914
|
1.3236421
|
1.2704616
|
1.2172365
|
1.1639540
|
1.1106017
|
1.0571677
|
1.0036407
|
0.9500098
|
0.8962647
|
0.8423958
|
0.7883939
|
0.7342505
|
0.6799576
|
0.6255079
|
0.5708946
|
0.5161119
|
0.4611542
|
0.4060169
|
0.3506960
|
0.2951883
|
0.2394911
|
0.1836026
|
0.1275218
|
0.0712501
|
0.0148566
|
-0.0415012
|
-0.0976640
|
-0.1534777
|
-0.2087932
|
-0.2634668
|
-0.3173597
|
-0.3703388
|
-0.4222756
|
-0.4730470
|
-0.5225349
|
-0.5706256
|
-0.6172104
|
-0.6621844
|
-0.7054470
|
-0.7469013
|
-0.7864534
|
-0.8240124
|
-0.8594900
|
-0.8927995
|
-0.9238560
|
-0.9525751
|
-0.9788731
|
-1.0026656
|
-1.0238675
|
-1.0423920
|
-1.0581499
|
-1.0710488
|
-1.0809928
|
-1.0878809
|
-1.0916338
|
-1.0923120
|
-1.0900196
|
-1.0848544
|
-1.0769087
|
-1.0662701
|
-1.0530223
|
-1.0372452
|
-1.0190162
|
-0.9984100
|
-0.9754999
|
-0.9503578
|
-0.9230550
|
-0.8936625
|
-0.8622516
|
-0.8288945
|
-0.7936641
|
-0.7566351
|
-0.7178839
|
-0.6774894
|
-0.6355327
|
-0.5920980
|
-0.5472723
|
-0.5011462
|
-0.4538137
|
-0.4053726
|
-0.3559245
|
-0.3055749
|
-0.2544336
|
-0.2026144
|
-0.1502353
|
|
E2f8
|
2.296814
|
2.231562
|
2.167264
|
2.103738
|
2.040818
|
1.978347
|
1.916182
|
1.854190
|
1.792249
|
1.7302520
|
1.6681000
|
1.6057073
|
1.5429999
|
1.4799154
|
1.4164035
|
1.3524259
|
1.2879566
|
1.2229813
|
1.1574983
|
1.0915178
|
1.0250618
|
0.9581644
|
0.8908713
|
0.8232392
|
0.7553359
|
0.6872394
|
0.6190376
|
0.5508276
|
0.4827144
|
0.4148108
|
0.3472360
|
0.2801144
|
0.2135748
|
0.1477489
|
0.0827703
|
0.0187729
|
-0.0441104
|
-0.1057489
|
-0.1660125
|
-0.2246585
|
-0.2813301
|
-0.3357335
|
-0.3876454
|
-0.4369068
|
-0.4834158
|
-0.5271208
|
-0.5680127
|
-0.6061183
|
-0.6414937
|
-0.6742179
|
-0.7043875
|
-0.7321113
|
-0.7575064
|
-0.7806944
|
-0.8017980
|
-0.8209385
|
-0.8382334
|
-0.8537950
|
-0.8677287
|
-0.8801318
|
-0.8910927
|
-0.9006901
|
-0.9089920
|
-0.9160556
|
-0.9219258
|
-0.9266354
|
-0.9302031
|
-0.9326332
|
-0.9339134
|
-0.9340243
|
-0.9329859
|
-0.9308186
|
-0.9275244
|
-0.9230883
|
-0.9174791
|
-0.9106493
|
-0.9025359
|
-0.8930594
|
-0.8821241
|
-0.8696169
|
-0.8554068
|
-0.8393436
|
-0.8212570
|
-0.8009553
|
-0.7782238
|
-0.7528242
|
-0.7244925
|
-0.6929383
|
-0.6578434
|
-0.6188613
|
-0.5756166
|
-0.5277050
|
-0.4746940
|
-0.4161241
|
-0.3515113
|
-0.2803502
|
-0.2021191
|
-0.1162855
|
-0.0223144
|
0.0803225
|
|
Onecut2
|
1.958698
|
1.896456
|
1.835369
|
1.775439
|
1.716666
|
1.659051
|
1.602593
|
1.547287
|
1.493130
|
1.4401190
|
1.3882466
|
1.3375068
|
1.2878923
|
1.2393952
|
1.1920067
|
1.1457175
|
1.1005178
|
1.0563972
|
1.0133448
|
0.9713494
|
0.9303994
|
0.8904830
|
0.8515878
|
0.8137016
|
0.7768118
|
0.7409056
|
0.7059701
|
0.6719926
|
0.6389600
|
0.6068594
|
0.5756779
|
0.5454027
|
0.5160210
|
0.4875201
|
0.4598876
|
0.4331112
|
0.4071786
|
0.3820780
|
0.3577951
|
0.3342067
|
0.3110498
|
0.2880650
|
0.2650065
|
0.2416421
|
0.2177537
|
0.1931374
|
0.1676048
|
0.1409839
|
0.1131204
|
0.0838788
|
0.0531446
|
0.0208248
|
-0.0131497
|
-0.0488232
|
-0.0862138
|
-0.1253125
|
-0.1660822
|
-0.2084579
|
-0.2523461
|
-0.2976255
|
-0.3441482
|
-0.3917411
|
-0.4402078
|
-0.4893314
|
-0.5388777
|
-0.5885983
|
-0.6382352
|
-0.6875250
|
-0.7362031
|
-0.7839880
|
-0.8305087
|
-0.8754150
|
-0.9184222
|
-0.9593088
|
-0.9979126
|
-1.0341260
|
-1.0678912
|
-1.0991936
|
-1.1280562
|
-1.1545334
|
-1.1787051
|
-1.2006715
|
-1.2205475
|
-1.2384588
|
-1.2545374
|
-1.2689182
|
-1.2817365
|
-1.2931250
|
-1.3032126
|
-1.3121223
|
-1.3199708
|
-1.3268672
|
-1.3329130
|
-1.3382017
|
-1.3428190
|
-1.3468428
|
-1.3503435
|
-1.3533846
|
-1.3560228
|
-1.3583087
|
|
Gm5141
|
1.719215
|
1.685090
|
1.651235
|
1.617614
|
1.584193
|
1.550940
|
1.517823
|
1.484811
|
1.451877
|
1.4189899
|
1.3861248
|
1.3532552
|
1.3203565
|
1.2874053
|
1.2543791
|
1.2212566
|
1.1880179
|
1.1546439
|
1.1211169
|
1.0874203
|
1.0535387
|
1.0194579
|
0.9851650
|
0.9506480
|
0.9158966
|
0.8809013
|
0.8456541
|
0.8101481
|
0.7743778
|
0.7383389
|
0.7020284
|
0.6654446
|
0.6285869
|
0.5914562
|
0.5540545
|
0.5163854
|
0.4784533
|
0.4402643
|
0.4018256
|
0.3631559
|
0.3242872
|
0.2852521
|
0.2460829
|
0.2068114
|
0.1674689
|
0.1280861
|
0.0886932
|
0.0493197
|
0.0099946
|
-0.0292538
|
-0.0683981
|
-0.1074114
|
-0.1462676
|
-0.1849414
|
-0.2234082
|
-0.2616443
|
-0.2996269
|
-0.3373337
|
-0.3747437
|
-0.4118365
|
-0.4485925
|
-0.4849931
|
-0.5210207
|
-0.5566582
|
-0.5918898
|
-0.6267004
|
-0.6610758
|
-0.6950025
|
-0.7284683
|
-0.7614600
|
-0.7939581
|
-0.8259424
|
-0.8573947
|
-0.8882988
|
-0.9186403
|
-0.9484068
|
-0.9775877
|
-1.0061738
|
-1.0341580
|
-1.0615343
|
-1.0882983
|
-1.1144473
|
-1.1399794
|
-1.1648945
|
-1.1891932
|
-1.2128774
|
-1.2359501
|
-1.2584151
|
-1.2802771
|
-1.3015418
|
-1.3222155
|
-1.3423050
|
-1.3618181
|
-1.3807630
|
-1.3991482
|
-1.4169830
|
-1.4342769
|
-1.4510398
|
-1.4672818
|
-1.4830134
|
|
Zbtb40
|
1.878808
|
1.826993
|
1.775823
|
1.725297
|
1.675412
|
1.626167
|
1.577559
|
1.529585
|
1.482244
|
1.4355311
|
1.3894444
|
1.3439804
|
1.2991356
|
1.2549066
|
1.2112897
|
1.1682812
|
1.1258770
|
1.0840733
|
1.0428659
|
1.0022506
|
0.9622230
|
0.9227787
|
0.8839133
|
0.8456221
|
0.8079005
|
0.7707438
|
0.7341472
|
0.6981059
|
0.6626149
|
0.6276695
|
0.5932645
|
0.5593950
|
0.5260559
|
0.4932422
|
0.4609488
|
0.4291705
|
0.3979023
|
0.3671390
|
0.3368746
|
0.3070721
|
0.2776536
|
0.2485419
|
0.2196633
|
0.1909471
|
0.1623262
|
0.1337364
|
0.1051172
|
0.0764109
|
0.0475632
|
0.0185231
|
-0.0107572
|
-0.0403220
|
-0.0702123
|
-0.1004656
|
-0.1311159
|
-0.1621935
|
-0.1937250
|
-0.2257334
|
-0.2582378
|
-0.2912533
|
-0.3247913
|
-0.3588588
|
-0.3934591
|
-0.4285913
|
-0.4642503
|
-0.5004272
|
-0.5371086
|
-0.5742772
|
-0.6119119
|
-0.6499767
|
-0.6883765
|
-0.7270005
|
-0.7657431
|
-0.8045043
|
-0.8431896
|
-0.8817105
|
-0.9199843
|
-0.9579342
|
-0.9954892
|
-1.0325842
|
-1.0691598
|
-1.1051624
|
-1.1405438
|
-1.1752609
|
-1.2092762
|
-1.2425567
|
-1.2750743
|
-1.3068055
|
-1.3377308
|
-1.3678349
|
-1.3971061
|
-1.4255364
|
-1.4531210
|
-1.4798579
|
-1.5057482
|
-1.5307953
|
-1.5550051
|
-1.5783854
|
-1.6009460
|
-1.6226983
|
|
Wdhd1
|
1.937591
|
1.883816
|
1.830725
|
1.778310
|
1.726563
|
1.675474
|
1.625036
|
1.575241
|
1.526079
|
1.4775436
|
1.4296264
|
1.3823196
|
1.3356156
|
1.2895067
|
1.2439854
|
1.1990444
|
1.1546764
|
1.1108742
|
1.0676307
|
1.0249390
|
0.9827922
|
0.9411834
|
0.9001061
|
0.8595535
|
0.8195193
|
0.7799969
|
0.7409801
|
0.7024627
|
0.6644384
|
0.6269012
|
0.5898452
|
0.5532644
|
0.5171531
|
0.4815055
|
0.4463160
|
0.4115789
|
0.3772889
|
0.3434405
|
0.3100278
|
0.2770229
|
0.2443694
|
0.2120120
|
0.1798987
|
0.1479802
|
0.1162106
|
0.0845468
|
0.0529485
|
0.0213788
|
-0.0101967
|
-0.0418092
|
-0.0734870
|
-0.1052555
|
-0.1371372
|
-0.1691515
|
-0.2013149
|
-0.2336409
|
-0.2661401
|
-0.2988201
|
-0.3316853
|
-0.3647375
|
-0.3979753
|
-0.4313945
|
-0.4649879
|
-0.4987454
|
-0.5326544
|
-0.5666993
|
-0.6008620
|
-0.6351216
|
-0.6694550
|
-0.7038290
|
-0.7381691
|
-0.7723910
|
-0.8064154
|
-0.8401688
|
-0.8735828
|
-0.9065944
|
-0.9391461
|
-0.9711856
|
-1.0026659
|
-1.0335448
|
-1.0637855
|
-1.0933554
|
-1.1222271
|
-1.1503770
|
-1.1777860
|
-1.2044388
|
-1.2303240
|
-1.2554334
|
-1.2797622
|
-1.3033085
|
-1.3260734
|
-1.3480602
|
-1.3692748
|
-1.3897250
|
-1.4094206
|
-1.4283731
|
-1.4465952
|
-1.4641012
|
-1.4809064
|
-1.4970271
|
|
Mybl1
|
1.817529
|
1.787012
|
1.756658
|
1.726375
|
1.696075
|
1.665671
|
1.635081
|
1.604226
|
1.573029
|
1.5414185
|
1.5093243
|
1.4766814
|
1.4434278
|
1.4095057
|
1.3748613
|
1.3394449
|
1.3032113
|
1.2661199
|
1.2281346
|
1.1892244
|
1.1493634
|
1.1085308
|
1.0667113
|
1.0238953
|
0.9800786
|
0.9352631
|
0.8894566
|
0.8426727
|
0.7949314
|
0.7462586
|
0.6966864
|
0.6462529
|
0.5950025
|
0.5429852
|
0.4902571
|
0.4368797
|
0.3829199
|
0.3284500
|
0.2735488
|
0.2183782
|
0.1631969
|
0.1082511
|
0.0537659
|
-0.0000551
|
-0.0530290
|
-0.1049940
|
-0.1558080
|
-0.2053484
|
-0.2535109
|
-0.3002085
|
-0.3453707
|
-0.3889418
|
-0.4308799
|
-0.4711558
|
-0.5097515
|
-0.5466593
|
-0.5818802
|
-0.6154230
|
-0.6473033
|
-0.6775420
|
-0.7061649
|
-0.7332011
|
-0.7586828
|
-0.7826439
|
-0.8051198
|
-0.8261463
|
-0.8457590
|
-0.8639929
|
-0.8808818
|
-0.8964670
|
-0.9108367
|
-0.9240875
|
-0.9363072
|
-0.9475758
|
-0.9579666
|
-0.9675465
|
-0.9763770
|
-0.9845144
|
-0.9920109
|
-0.9989147
|
-1.0052704
|
-1.0111197
|
-1.0165013
|
-1.0214516
|
-1.0260047
|
-1.0301929
|
-1.0340466
|
-1.0375948
|
-1.0408652
|
-1.0438843
|
-1.0466773
|
-1.0492690
|
-1.0516828
|
-1.0539420
|
-1.0560688
|
-1.0580851
|
-1.0600122
|
-1.0618711
|
-1.0636823
|
-1.0654659
|
|
Tax1bp1
|
1.702802
|
1.673959
|
1.645138
|
1.616310
|
1.587451
|
1.558534
|
1.529534
|
1.500425
|
1.471181
|
1.4417780
|
1.4121904
|
1.3823934
|
1.3523624
|
1.3220731
|
1.2915011
|
1.2606224
|
1.2294133
|
1.1978501
|
1.1659096
|
1.1335686
|
1.1008041
|
1.0675937
|
1.0339149
|
0.9997456
|
0.9650639
|
0.9298484
|
0.8940777
|
0.8577309
|
0.8207873
|
0.7832267
|
0.7450290
|
0.7061746
|
0.6666442
|
0.6264189
|
0.5854801
|
0.5438097
|
0.5013901
|
0.4582038
|
0.4142352
|
0.3695140
|
0.3241314
|
0.2781816
|
0.2317580
|
0.1849529
|
0.1378576
|
0.0905623
|
0.0431562
|
-0.0042728
|
-0.0516380
|
-0.0988535
|
-0.1458349
|
-0.1924988
|
-0.2387630
|
-0.2845464
|
-0.3297690
|
-0.3743519
|
-0.4182173
|
-0.4612884
|
-0.5034894
|
-0.5447455
|
-0.5849825
|
-0.6241276
|
-0.6621081
|
-0.6988527
|
-0.7342902
|
-0.7683504
|
-0.8009631
|
-0.8320591
|
-0.8615690
|
-0.8894397
|
-0.9157039
|
-0.9404230
|
-0.9636571
|
-0.9854657
|
-1.0059073
|
-1.0250395
|
-1.0429194
|
-1.0596032
|
-1.0751467
|
-1.0896048
|
-1.1030321
|
-1.1154826
|
-1.1270100
|
-1.1376673
|
-1.1475075
|
-1.1565828
|
-1.1649456
|
-1.1726476
|
-1.1797404
|
-1.1862756
|
-1.1923042
|
-1.1978773
|
-1.2030459
|
-1.2078606
|
-1.2123722
|
-1.2166310
|
-1.2206877
|
-1.2245925
|
-1.2283957
|
-1.2321476
|
heatmap_matrix_q_value_0.01 <- left_join(select(transcription_factors_table_q_value_0.01, gene, pval, qval, num_cells_expressed), heatmap_matrix_q_value_0.01)
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "3-forebrain_oligodendrocytes_joint_cortex_clusters_14_22-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=TRUE, return_matrix = TRUE)

ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_0.01, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "3_forebrain_oligodendrocytes_joint_forebrain_differential_gene_test_analysis_qval_0.01_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Plotting of transcription factors differentially expressed in pseudotime
Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
